Simulation with quantum mechanics/molecular mechanics for drug discovery

Evidence for a Boat Conformation at the Transition State of GH76 α-1,6-Mannanases-Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism

(2015) Andrew J. Thompson et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations

(2015) Albert Ardèvol et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Application of Docking and QM/MM-GBSA Rescoring to Screen for Novel Myt1 Kinase Inhibitors

(2014) Kanin Wichapong et al.   Journal of Chemical Information and Modeling

Crystal Structures of Substrate-Free and Nitrosyl Cytochrome P450cin: Implications for O2 Activation

(2012) Yarrow Madrona et al.   BIOCHEMISTRY

Essential role of glutamate 317 in galactosyl transfer by α3GalT: a computational study

(2012) Hansel Gómez et al.   CARBOHYDRATE RESEARCH

Is inhibition process better described with MD(QM/MM) simulations? The case of urokinase type plasminogen activator inhibitors

(2012) Florent Barbault et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Retaining Glycosyltransferase Mechanism Studied by QM/MM Methods: Lipopolysaccharyl-α-1,4-galactosyltransferase C Transfers α-Galactose via an Oxocarbenium Ion-like Transition State

(2012) Hansel Gómez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Developing inhibitors of glycan processing enzymes as tools for enabling glycobiology

(2012) Tracey M Gloster et al.   Nature Chemical Biology

Reduction Potentials and Acidity Constants of Mn Superoxide Dismutase Calculated by QM/MM Free-Energy Methods

(2011) Jimmy Heimdal et al.   CHEMPHYSCHEM

Synthesis of purin-2-yl and purin-6-yl-aminoglucitols as C-nucleosidic ATP mimics and biological evaluation as FGFR3 inhibitors

(2011) Lotfi Tak-Tak et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

DynamO: a free ${\cal O}$(N) general event-driven molecular dynamics simulator

(2011) M. N. Bannerman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods

(2010) Kara E. Ranaghan et al.   INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY

QM/MM X-ray refinement of zinc metalloenzymes

(2010) Xue Li et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

Advances in Quantum and Molecular Mechanical (QM/MM) Simulations for Organic and Enzymatic Reactions

(2009) Orlando Acevedo et al.   ACCOUNTS OF CHEMICAL RESEARCH

QM/MM Methods for Biomolecular Systems

(2009) Hans Martin Senn et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations

(2009) Sason Shaik et al.   CHEMICAL REVIEWS

Molecular modeling study of binding site selectivity of TQMP to G-quadruplex DNA

(2009) Li Aixiao et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach

(2009) Marius Retegan et al.   Journal of Chemical Information and Modeling

Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions

(2009) Robert S. Paton et al.   Journal of Chemical Information and Modeling

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

High Level QM/MM Modeling of the Formation of the Tetrahedral Intermediate in the Acylation of Wild Type and K73A Mutant TEM-1 Class A β-Lactamase†

(2009) Johannes C. Hermann et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective†

(2009) Gustavo de M. Seabra et al.   JOURNAL OF PHYSICAL CHEMISTRY A

ONIOM study of the nonbonding interaction of the 2PU inhibitor with the CDK2 and CDK4 cyclin-dependant kinases

(2008) Aixiao Li et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

The implementation of a fast and accurate QM/MM potential method in Amber

(2007) Ross C. Walker et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY